Genomic Surveillance of SARS-CoV-2 Variants Circulating in Rajasthan in 2025

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has undergone significant evolutionary changes since its onset, resulting in the emergence of multiple variants with distinct genetic profiles and public health implications. Numerous genetic modifications have occurred in the virus since it first appeared, leading to the development of several variants with varying degrees of virulence, transmissibility, and immunological escape potential.

A total of 602 throat/nasopharyngeal swabs of SARS-CoV-2-positive patients were received at Sawai Man Singh Medical College (SMSMC), Jaipur, India, from April 30, 2025, to September 5, 2025, for next-generation sequencing, of which 373 samples having a Ct value ≤ 25 were further processed for sequencing.

Among the 373 lineages identified, XFG was the predominant lineage and was detected in 182 (48.8%) cases, including​​​​​​​ XFG (85), XFG.3 (95), and XFG.3.1 (2). Other lineages identified were PY.1 (65, 17.43%), LF.7 and its sublineages (61, 16.35%), JN.1 and its sublineages (23, 6.17%), PY.2 (23, 6.17%), BA.2 and its sublineages (8, 2.14%), PL.1.1 (3, 0.8%), LP.8.1 (2, 0.53%), NB.1.8.1 (2, 0.53%), XFC.1 (1, 0.27%), XFJ (1, 0.27%), PQ.7 (1, 0.27%) and IN.1.16.1 (1, 0.27%). Among the total positive cases identified, 55.76% were males and 44.24% were females. Regarding age distribution, 10.19% were aged <18 years, 68.90% were aged 19-59 years, and 20.91% were aged ≥60 years. Overall, 21.18% of cases were asymptomatic, whereas 78.82% were symptomatic. Reinfection was observed in 28.95% (108) of cases. ​​​​​​​​​​​​​​​​​​Most positive cases were reported from the Jaipur district. The majority of positive cases (88.47%, 330) had already been vaccinated. Comorbidities or other underlying conditions were present in 25.74% (96) of patients. Hospitalization was required in 25.47% (95) of cases, and death due to COVID was reported in three cases.

The highest upsurge in COVID cases during the study period was due to the XFG variant, which is a recombinant hybrid of the LF.7 and LP.8.1.2 Omicron subvariants. Continuous genomic surveillance helps in detecting real-time viral recombination and mapping spike protein mutations that lead to the emergence of such variants. Genomic surveillance revealed a wide range of SARS-CoV-2 variants in Rajasthan, with implications for public health response and vaccination strategies. The study underscores the critical importance of sustained genomic surveillance programs in Rajasthan to track viral evolution in near real-time, mitigate transmission risks, and strengthen pandemic preparedness at both regional and national levels.